Allyl chloroformate is primarily used as a reagent in organic synthesis, especially in the protection of functional groups such as amines and alcohols. It reacts readily to form allyl carbamate (alloc) and allyl carbonate derivatives, which are useful protecting groups in peptide and nucleotide synthesis due to their stability under a variety of reaction conditions and selective removal via palladium-catalyzed deprotection.

It is also employed in the preparation of heterocyclic compounds and pharmaceutical intermediates. Its ability to introduce allyloxy carbonyl groups makes it valuable in the development of complex molecules in medicinal chemistry. Additionally, it serves as a building block in the synthesis of agrochemicals and specialty polymers.

Due to its high reactivity and lachrymatory nature, it is handled with care in controlled environments, typically under inert atmosphere and with appropriate safety measures.